TB Profiler
This tool processes raw sequence data to infer strain type and identify known drug resistance markers.
A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.



This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.
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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).
Name: 5cc54d3a4e2da
Sample: 5cc54d3a4e2da

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Summary
ID: 5cc54d3a4e2da
Date: Sun Apr 28 07:51:38 2019
Strain: lineage2;lineage4.3.1;lineage3.1.2.2
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage4.3.1Euro-American (LAM)LAM9None
lineage3.1.2.2East-African-IndianCASRD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7391c.90C>T1.000
gyrA7394c.93T>C1.000
gyrA7397c.96G>C1.000
gyrA7406c.105G>C1.000
gyrA7412c.111C>G1.000
gyrA7418c.117C>T1.000
gyrA7433c.132G>A1.000
gyrA7442c.141G>C1.000
gyrA7457c.156T>C1.000
gyrA7463c.162G>C1.000
gyrA7472c.171T>C1.000
gyrA7475c.174A>G1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7499c.198G>C1.000
gyrA7526c.225G>C1.000
gyrA7532c.231T>G1.000
gyrA7541c.240C>G1.000
gyrA7547c.246C>T1.000
gyrA7565c.264C>T1.000
gyrA7569p.Ala90Ser1.000
gyrA7585p.Ser95Thr1.000
gyrA8294c.993T>C1.000
gyrA8324c.1023T>C1.000
gyrA8327c.1026C>G1.000
gyrA8339c.1038A>G1.000
gyrA8340p.Ala347Ser1.000
gyrA8354c.1053G>C1.000
gyrA8366c.1065G>C1.000
gyrA8372c.1071G>T1.000
rpoB760181c.375T>C1.000
rpoB760184c.378A>G1.000
rpoB760196c.390C>G1.000
rpoB760235c.429T>C1.000
rpoB760244c.438G>C1.000
rpoB760283c.477G>C1.000
rpoB760298c.492G>C1.000
rpoB760430c.624T>C1.000
rpoB760433c.627C>T1.000
rpoB760457c.651C>T1.000
rpoB760463c.657C>T1.000
rpoB761213c.1407G>C1.000
rpoB761249c.1443A>G1.000
rpoB761261c.1455G>T1.000
rpoB761264c.1458C>G1.000
rpoB761282c.1476C>T1.000
rpoB761288c.1482G>T1.000
rpoB761318c.1512G>T1.000
rpoB761327c.1521A>G1.000
rpoB761330c.1524G>C1.000
rpoB761552c.1746G>C1.000
rpoB761555c.1749G>C1.000
rpoB761558c.1752C>G1.000
rpoB761570c.1764T>C1.000
rpoB761573c.1767C>G1.000
rpoB761579c.1773G>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761969c.2163G>A1.000
rpoB762008c.2202C>T1.000
rpoB762014c.2208C>T1.000
rpoB762047c.2241G>A1.000
rpoB762053c.2247T>C1.000
rpoB762065c.2259T>C1.000
rpoB762083c.2277T>C1.000
rpoB762086c.2280G>C1.000
rpoB762101c.2295C>G1.000
rpoB762114p.Ile770Val1.000
rpoB762158c.2352G>C1.000
rpoB762185c.2379G>C1.000
rpoB762224c.2418C>G1.000
rpoB762233c.2427G>C1.000
rpoB762245c.2439G>C1.000
rpoB762833c.3027C>T1.000
rpoB762839c.3033G>A1.000
rpoB762857c.3051C>G1.000
rpoB762863c.3057T>C1.000
rpoB762879p.Met1025Leu1.000
rpoB762917c.3111C>G1.000
rpoB762920c.3114C>T1.000
rpoB762929c.3123G>C1.000
rpoB762959c.3153G>C1.000
rpoB762962c.3156C>T1.000
rpoB762995c.3189G>T0.917
rpoB763004c.3198G>A1.000
rpoB763007c.3201C>T1.000
rpoB763022c.3216C>G1.000
rpoB763028c.3222T>C1.000
rpoB763031c.3225T>G1.000
rpoB763053c.3247T>C1.000
rpoB763070c.3264T>C1.000
rpoB763085c.3279C>G1.000
rpoB763103c.3297G>C1.000
rpoB763115c.3309T>C1.000
rpoB763127c.3321G>C1.000
rpoB763130c.3324G>A1.000
rpoB763133c.3327G>C1.000
rpoB763136c.3330C>T1.000
rpoB763142c.3336C>G1.000
rpoB763160c.3354G>T1.000
rpoC763456c.87A>G1.000
rpoC763468c.99G>C1.000
rpoC763486c.117T>C1.000
rpoC763492c.123G>T1.000
rpoC763528c.159G>A1.000
rpoC763546c.177A>G1.000
rpoC763558c.189C>T1.000
rpoC763570c.201G>C1.000
rpoC763573c.204G>C1.000
rpoC763594c.225C>T1.000
rpoC763603c.234C>T1.000
rpoC763615c.246G>C1.000
rpoC763618c.249C>T1.000
rpoC763633c.264T>C1.000
rpoC763660c.291T>G1.000
rpoC763666c.297G>A1.000
rpoC763675c.306C>G1.000
rpoC763765c.396T>G1.000
rpoC763792p.Glu141Asp1.000
rpoC763807c.438T>C1.000
rpoC763813c.444C>G1.000
rpoC764500c.1131C>G1.000
rpoC764521c.1152T>C1.000
rpoC764536c.1167G>T1.000
rpoC764539c.1170C>G1.000
rpoC764575c.1206T>G1.000
rpoC764605c.1236G>C1.000
rpoC764611c.1242G>T1.000
rpoC764623c.1254C>G1.000
rpoC764626c.1257C>T1.000
rpoC764632c.1263T>C1.000
rpoC764650c.1281G>T1.000
rpoC764701c.1332C>G1.000
rpoC764713c.1344G>T1.000
rpoC764716c.1347G>C1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764c.1395T>C1.000
rpoC764803c.1434C>T1.000
rpoC764809c.1440C>T1.000
rpoC764815c.1446A>G1.000
rpoC764824c.1455T>C1.000
rpoC764827c.1458G>C1.000
rpoC764851c.1482C>T1.000
rpoC764858c.1489T>C1.000
rpoC764869c.1500C>T1.000
rpoC764875c.1506C>T1.000
rpoC764878c.1509C>G1.000
rpoC764887c.1518G>C1.000
rpoC764888c.1519T>C1.000
rpoC764911c.1542A>G1.000
rpoC764912p.Met515Gln1.000
rpoC764932c.1563C>A0.938
rpoC764935c.1566T>C1.000
rpoC764948c.1579T>C1.000
rpoC764968c.1599T>C1.000
rpoC765466c.2097C>T1.000
rpoC765478c.2109T>C1.000
rpoC765480p.Tyr704Phe1.000
rpoC765496c.2127C>G1.000
rpoC765811c.2442T>G1.000
rpoC765814c.2445A>C1.000
rpoC765817c.2448G>C1.000
rpoC765823c.2454C>A1.000
rpoC765826c.2457T>C1.000
rpoC765835c.2466C>T1.000
rpoC765871c.2502T>C1.000
rpoC765875p.Val836Ile1.000
rpoC765886c.2517C>G1.000
rpoC765904c.2535C>G1.000
rpoC765908c.2539C>T1.000
rpsL781628c.69T>C1.000
rpsL781631c.72G>C1.000
rpsL781649c.90T>C1.000
rpsL781655c.96T>C1.000
rpsL781658c.99A>G1.000
rpsL781682c.123T>C1.000
rpsL781709c.150G>C1.000
rpsL781715c.156T>C1.000
rpsL781760c.201T>C1.000
rpsL781772c.213C>T1.000
rpsL781808c.249C>T1.000
rpsL781814c.255C>T1.000
rpsL781817c.258G>T1.000
rpsL781829c.270G>C1.000
rpsL781832c.273T>C1.000
rpsL781838c.279G>C1.000
rpsL781841c.282C>T1.000
rpsL781859c.300T>G1.000
rpsL781865c.306G>C1.000
rpsL781868c.309T>C1.000
rpsL781871c.312G>C1.000
rpsL781892c.333A>G1.000
rpsL781898c.339A>C1.000
rpsL781901c.342C>T1.000
rpsL781907c.348T>C1.000
rpsL781916c.357T>C1.000
rpsL781929p.Gly124Ser1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471933r.88ga>g1.000
rrs1471934r.89a>g1.000
rrs1471986r.141c>t1.000
rrs1472019r.174g>a1.000
rrs1472023r.178g>t1.000
rrs1472031r.186g>c1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472150r.305t>a1.000
rrs1472251r.406g>a1.000
rrs1472337r.492c>g1.000
rrs1472380r.535g>c1.000
rrs1472446r.601t>a0.950
rrs1472452r.607g>a0.974
rrs1472464r.619a>g1.000
rrs1472846r.1001c>a1.000
rrs1472847r.1002g>c0.941
rrs1472849r.1004c>g1.000
rrs1472850r.1005t>c1.000
rrs1472857r.1012a>g1.000
rrs1472858r.1013g>t1.000
rrs1472860r.1015c>g1.000
rrs1472861r.1016g>t1.000
rrs1472973r.1128a>t1.000
rrs1473104r.1259c>t0.972
rrs1473110r.1265t>g1.000
rrs1473111r.1266a>g1.000
rrs1473120r.1275c>ct0.865
rrs1473123r.1278a>c1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt1.000
rrs1473301r.1456t>c1.000
rrl1473668r.11c>t1.000
rrl1473696r.39t>c1.000
rrl1473697r.40c>t1.000
rrl1473699r.42a>g1.000
rrl1473717r.60g>t0.963
rrl1473746r.89t>c1.000
rrl1473758r.101g>t1.000
rrl1473770r.113t>g1.000
rrl1473788r.131a>g1.000
rrl1473876r.219g>a1.000
rrl1473887r.230t>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1474135r.478g>a0.957
rrl1474140r.483c>t0.957
rrl1474151r.494c>t0.960
rrl1474174r.517a>g0.962
rrl1474181r.524c>t1.000
rrl1474183r.526t>c1.000
rrl1474185r.528g>a1.000
rrl1474186r.529a>g1.000
rrl1474249r.592g>t1.000
rrl1474266r.609t>c1.000
rrl1474269r.612c>t1.000
rrl1474310r.653t>g1.000
rrl1474362r.705a>g1.000
rrl1474446r.789c>t1.000
rrl1474673r.1016t>c1.000
rrl1474676r.1019t>a1.000
rrl1474677r.1020a>g1.000
rrl1474720r.1063c>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1474932r.1275c>t1.000
rrl1475031r.1374g>t1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t1.000
rrl1475120r.1463g>t1.000
rrl1475315r.1658a>t1.000
rrl1475353r.1696a>t1.000
rrl1475354r.1697a>g1.000
rrl1475355r.1698c>t1.000
rrl1475363r.1706c>t1.000
rrl1475369r.1712g>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>t1.000
rrl1475452r.1795c>a1.000
rrl1475479r.1822c>g1.000
rrl1475483r.1826c>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>t1.000
rrl1475762r.2105g>t1.000
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c1.000
rrl1475765r.2108a>g1.000
rrl1475775r.2118g>a1.000
rrl1475988r.2331a>g1.000
rrl1475991r.2334t>c1.000
rrl1475995r.2338g>a1.000
rrl1476088r.2431a>c0.947
rrl1476099r.2442a>g0.933
rrl1476103r.2446c>g0.933
rrl1476105r.2448g>a0.933
rrl1476106r.2449a>t0.933
rrl1476110r.2453g>c0.933
rrl1476115r.2458t>c0.941
rrl1476131r.2474c>t0.964
rrl1476160r.2503t>c1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>g0.971
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476529r.2872a>g1.000
rrl1476540r.2883c>t1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>c1.000
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>c1.000
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t1.000
rrl1476693r.3036g>a1.000
rrl1476695r.3038t>a1.000
rpsA1833616c.75A>C1.000
rpsA1833619c.78A>C1.000
rpsA1833628c.87G>C1.000
rpsA1833634c.93G>A1.000
rpsA1833894p.Ala118Glu1.000
rpsA1833904c.363G>A1.000
rpsA1833928c.387G>C1.000
rpsA1833949c.408T>C1.000
rpsA1833970c.429G>T1.000
rpsA1833976c.435C>T1.000
rpsA1833979c.438T>C1.000
rpsA1833991c.450C>A1.000
rpsA1834000c.459G>C1.000
rpsA1834009c.468C>T1.000
rpsA1834012c.471G>T1.000
rpsA1834015c.474G>C1.000
rpsA1834021c.480C>T1.000
rpsA1834030c.489C>G1.000
rpsA1834078c.537C>T1.000
rpsA1834097c.556T>A1.000
rpsA1834102c.561T>C1.000
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C1.000
rpsA1834213c.672G>C1.000
rpsA1834234c.693G>C1.000
rpsA1834240c.699T>C1.000
rpsA1834246c.705G>C1.000
rpsA1834249c.708T>C1.000
rpsA1834252c.711C>G1.000
rpsA1834261c.720A>G1.000
rpsA1834264c.723G>C1.000
rpsA1834279c.738C>T1.000
rpsA1834297c.756C>T1.000
rpsA1834303c.762T>G1.000
rpsA1834366c.825A>G1.000
rpsA1834411c.870T>C1.000
rpsA1834423c.882G>T1.000
rpsA1834451c.910T>C1.000
rpsA1834456c.915T>G1.000
rpsA1834606c.1065C>T1.000
rpsA1834609c.1068T>C1.000
rpsA1834619c.1078T>C1.000
rpsA1834622c.1081T>A1.000
rpsA1834633c.1092A>G1.000
rpsA1834639c.1098T>C1.000
rpsA1834666c.1125G>C1.000
rpsA1834667p.Ala376Ser1.000
rpsA1834690c.1149T>C1.000
rpsA1834732c.1191T>C1.000
rpsA1834738c.1197A>G1.000
rpsA1834753c.1212T>C1.000
rpsA1834756c.1215G>A1.000
rpsA1834759c.1218A>C1.000
rpsA1834765p.Glu408Asp1.000
rpsA1834774c.1233C>G1.000
rpsA1834776p.Ala412Glu1.000
rpsA1834780c.1239A>G1.000
rpsA1834786c.1245A>G1.000
rpsA1834789c.1248T>C1.000
rpsA1834792c.1251G>C1.000
embC4240717c.855T>C1.000
embC4240768c.906G>A1.000
embC4240780c.918T>C1.000
embC4240783c.921G>C1.000
embC4240786c.924C>T1.000
embC4240789c.927T>C1.000
embC4240819c.957A>C1.000
embC4240828c.966G>A1.000
embC4240831c.969T>G1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)Specificity (%)
Isoniazid 92.8 (89.9-95.7)100 (100-100)
Rifampicin 96.2 (93.9-98.5)98.1 (96.8-99.4)
Ethambutal 88.7 (83.6-93.8)81.7 (77.6-85.8)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (29.6-90.4)68.7 (52.6-84.8)
Ofloxacin 85.5 (79.1-91.9)94.9 (91.8-98.0)
Amikacin 82.9 (74.4-91.4)98.3 (96.0-100)
Capreomycin 60.7 (50.6-70.8)90.7 (87.2-94.2)
Kanamycin 87.3 (81.3-93.3)93.4 (89.9-96.9)
Para-aminosalisylic acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
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